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PubMed1985

Classification of orbiviruses: a need for supergroups of genera.

There has been concern that the present nomenclature system for the members of the Reoviridae family, and particularly the Orbivirus genus, does not represent the actual relationships exhibited between the members. In order to follow the conventions established by the International Committee for the Taxonomy of Viruses (ICTV), it is tentatively proposed that the present Reoviridae genera be upgraded in status to the following sub-families: reovirinae, orbivirinae, Fijivirinae, cypovirinae, rotavirinae, coltivirinae and phytoreovirinae. Below the sub-family level, divisions of genus (equivalent to superserogroup, serocomplex or supergroup), sub-genus (equivalent to serogroup), species (equivalent to serotype or virus), and variant (equivalent to sub-serotype or genotype) could be created. In the orbivirinae this would result in 2 genera of cyanovirus (bluetongue, epizootic hemorrhagic disease, Eubenangee and Palyam sub-genera) and Kemerovovirus (Chenunda, Great Island, Kemerovo and Wad Medani sub-genera) and a number of ungrouped sub-genera (African horsesickness, Changuinola, Corriparta, equine encephalosis, Wallal and Warrego sub-genera and the remaining ungrouped viruses). It is hoped that further biochemical studies shall confirm these groupings at a more fundamental level and eventually a system recognising the double-stranded RNA gene product relationships shall evolve.

Bluetongue virus↗
PubMed1993

Safe biotechnology (5). Recommendations for safe work with animal and human cell cultures concerning potential human pathogens.

The benefits of using animal or human cell cultures have been clearly demonstrated in diagnostic and therapeutic research and in their application for manufacturing. Cell cultures serve as a tools for the production of vaccines, receptors, enzymes, monoclonal antibodies and recombinant DNA-derived proteins. They represent an integral part of drug development for which corresponding facilities, equipment and manufacturing processes are required. Although the cells themselves offer no particular risk to workers in laboratories and production areas or to the environment, the cell cultures may be contaminated with viruses, mycoplasma, bacteria, yeast and fungi or might contain endogenous viruses. The containment level for animal and human cells is therefore determined by the risk class of these agents. The history of animal and human cell cultures has proved that they can be handled safely. The recommendations in this publication concern the safe handling of cell cultures (tissue explants, primary cell cultures) and permanent cell lines of animal and human origin. A classification system of safety precautions has been elaborated according to the potential for contamination with the pathogenic agents involved.

Animal Population Groups↗
PubMed1984

Characterization of a cytoplasmic polyhedrosis virus infecting Manduca sexta.

A cytoplasmic polyhedrosis virus (CPV) infecting Manduca sexta was characterized. The genome consisted of ten equimolar RNA segments ranging in estimated molecular mass from 0.7 to 3.84 Mdaltons and with a total estimated molecular mass of 21.75 Mdaltons . The sizes of the individual RNA segments provisionally placed this CPV within the type 8 classification of Payne and Rivers. The polyhedrin protein had an estimated molecular mass of 28 kdaltons . Six virion-associated proteins were observed, ranging in size from 27.1 to 160 kdaltons . The RNA and protein profiles were compared to profiles observed from two other CPVs infecting Orgyia pseudotsugata and Bombyx mori. In addition, the nucleic acid sequence homology, using 32P-labeled cDNA to the total M. sexta CPV genome, demonstrated no homology with the B. mori CPV or the O. pseudotsugata CPV. The M. sexta CPV was transmitted by per os inoculation to O. pseudotsugata larvae.

Animals↗
PubMed1996

Viroids proper can be distinguished from hammerhead viroids and satellite RNAs through their dinucleotide composition.

G + C-rich viroids proper exhibit a unique dinucleotide composition in that AU and UA are much less frequent than expected. Thus, evaluation of the dinucleotide pattern allows a quick discrimination between viroids proper and similar RNAs from plants, such as hammerhead-containing viroids, satellite RNAs, and defective interfering RNAs. In addition to sequence alignment, this method might be useful for the classification of a newly found small RNA replicon.

Base Composition↗
PubMed2005

Fast rotational matching of single-particle images.

The presence of noise and absence of contrast in electron micrographs lead to a reduced resolution of the final 3D reconstruction, due to the inherent limitations of single-particle image alignment. The fast rotational matching (FRM) algorithm was introduced recently for an accurate alignment of 2D images under such challenging conditions. Here, we implemented this algorithm for the first time in a standard 3D reconstruction package used in electron microscopy. This allowed us to carry out exhaustive tests of the robustness and reliability in iterative orientation determination, classification, and 3D reconstruction on simulated and experimental image data. A classification test on GroEL chaperonin images demonstrates that FRM assigns up to 13% more images to their correct reference orientation, compared to the classical self-correlation function method. Moreover, at sub-nanometer resolution, GroEL and rice dwarf virus reconstructions exhibit a remarkable resolution gain of 10-20% that is attributed to the novel image alignment kernel.

Algorithms↗
PubMed2001

Primary effusion lymphoma: a liquid phase lymphoma of fluid-filled body cavities.

Primary effusion lymphoma (PEL) is a B-cell neoplasm characterized by infection of the tumor clone by human herpesvirus type-8/Kaposi's sarcoma-associated herpesvirus (HHV-8/KSHV) and by liquid growth in fluid-filled body spaces. During its entire clinical course, the lymphoma tends to remain localized to the serous body cavities with no formation of solid tumor masses. The epidemiology of PEL points to a close link with underlying immunodeficiency of the host, as most cases develop in individuals severely immunocompromised because of preexisting acquired immunodeficiency syndrome. The histogenesis and pathogenesis of PEL have been clarified to a sizeable extent by intensive investigations performed since the disease recognition in 1995. PEL is composed of postgerminal center B cells, which bridge immunoblastic and anaplastic features and typically display a non-B, non-T phenotype consistent with late stages of B-cell differentiation. HHV-8/KSHV is thought to play a major role in PEL pathogenesis via expression of several viral latent genes, which have the potential to affect B-cell growth. Other factors involved in PEL pathogenesis include deregulation of cytokine and growth factor autocrine loops, molecular alterations of the tumor DNA, cell cycle abnormalities, stimulation and selection by antigen, and infection by Epstein-Barr virus, which occurs in 70% of PEL cases. In the years since the disease discovery, the distinctiveness of the biological and clinicopathological features of PEL has prompted its recognition as an independent lymphoma category by the World Health Organization classification system of hematologic neoplasms.

Diagnosis, Differential↗
PubMedDate not supplied

Classification and regression trees--studies of HIV reverse transcriptase inhibitors.

In this paper, the application of Classification And Regression Trees (CART) is presented for the analysis of biological activity of Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs). The data consist of the biological activities, expressed as pIC50, of 208 NNRTIs against wild-type HIV virus (HIV-1) and four mutant strains (181C, 103N, 100I, 188L) and the computed interaction energies with the Reverse Transcriptase (RT) binding pocket. CART explains the observed biological activity of NNRTIs in terms of interactions with individual amino acids in the RT binding pocket, i.e., the original data variables.

Algorithms↗
PubMed2006

Genetics of hepatocellular tumors.

Numerous genetic alterations are accumulated during the process of hepatocarcinogenesis. These genetic alterations can be divided into two groups. The first set of genetic alterations is specific of hepatocellular tumor risk factors. It includes integration of hepatitis B virus (HBV) DNA, R249S TP53 (tumor protein p53) mutation in aflatoxin B1-exposed patients, KRAS mutations related to vinyl chloride exposure, hepatocyte nuclear factor 1alpha (HNF1alpha) mutations associated to hepatocellular adenomas and adenomatosis polyposis coli (APC) germline mutations predisposing to hepatoblastomas. The second set of genetic alterations are etiological nonspecific, it includes recurrent gains and losses of chromosomes, alteration of TP53 gene, activation of WNT/beta-catenin pathway through CTNNB1/beta-catenin and AXIN (axis inhibition protein) mutations, inactivation of retinoblastoma and IGF2R (insulin-like growth factor 2 receptor) pathways through inactivation of RB1 (retinoblastoma 1), P16 and IGF2R. Comprehensive analyses of these genetic alterations have defined two pathways of hepatocarcinogenesis according to the presence or the absence of chromosomal instability. Hepatitis B virus and poorly differentiated tumors are related to chromosome instable tumors associated with frequent TP53 mutations, whereas non-HBV and well-differentiated tumors are related to chromosomal stable samples that are frequently beta-catenin activated. These classifications have clinical relevance as genetic alterations may also be related to prognosis.

Carcinoma, Hepatocellular↗
PubMed1997

Conferring RNA polymerase activity to a DNA polymerase: a single residue in reverse transcriptase controls substrate selection.

The traditional classification of nucleic acid polymerases as either DNA or RNA polymerases is based, in large part, on their fundamental preference for the incorporation of either deoxyribonucleotides or ribonucleotides during chain elongation. The refined structure determination of Moloney murine leukemia virus reverse transcriptase, a strict DNA polymerase, recently allowed the prediction that a single amino acid residue at the active site might be responsible for the discrimination against the 2'OH group of an incoming ribonucleotide. Mutation of this residue resulted in a variant enzyme now capable of acting as an RNA polymerase. In marked contrast to the wild-type enzyme, the K(m) of the mutant enzyme for ribonucleotides was comparable to that for deoxyribonucleotides. The results are consistent with proposals of a common evolutionary origin for both classes of enzymes and support models of a common mechanism of nucleic acid synthesis underlying catalysis by all such polymerases.

Binding Sites↗
PubMed2006

Noninvasive diagnosis of liver fibrosis by ultrasonic transient elastography (Fibroscan).

Methods for diagnosing hepatic fibrosis have progressed significantly over the last few years--notably with the appearance of minimally invasive biological tests (which avoid the need for liver needle biopsy but nevertheless require a blood sample). Hepatic ultrasonic transient elastography (Fibroscan) is a new diagnostic method for hepatic fibrosis: it is totally noninvasive and gives an immediate result. Here, we review the currently available data on the use of the Fibroscan. Today's main field of application is chronic, viral hepatitis C, with areas under the receiver operation characteristic curve of 0.79-0.83, 0.90-0.91 and 0.91-0.97 for the diagnosis of F2, F3 and F4 fibrosis (defined according to the Metavir classification system), respectively. Furthermore, the Fibroscan enables the noninvasive diagnosis of cirrhosis (regardless of the latter's aetiology), with positive and negative predictive values of 70-95% and 77-95%, respectively. Chronic viral hepatitis B, HIV-hepatitis C virus and HIV-hepatitis B virus coinfections, alcohol-related liver diseases and intrahepatic cholestatic diseases are the device's other main fields of application in hepatology. Today, the Fibroscan is a reliable alternative for the noninvasive diagnosis of hepatic fibrosis. Various diagnostic strategies and performing cost/benefit analyses are now necessary, to assess fully the value of hepatic elastography relative to biological tests for hepatic fibrosis.

Chronic Disease↗
PubMed1993

Postoperative complications in patients with human immunodeficiency virus disease. Clinical data and a literature review.

OBJECTIVE: To compare complications after and outcome from surgical procedures between patients with human immunodeficiency virus (HIV) disease and a matched control population. DESIGN: Retrospective case review. SETTING: 476-bed university tertiary care center. PATIENTS: Of 343 patients diagnosed as having HIV disease between 1981 and September 1991, 26 (7.6 percent) were Walter Reed classifications system 3B or greater and underwent a surgical procedure with general anesthesia or, in the case of 2 patients, regional anesthesia, at the study hospital. These patients were matched to 26 control patients by severity of illness according to APACHE II severity of illness score and by age, sex, race, and anesthetic regimen. MEASUREMENTS AND RESULTS: The postoperative occurrence of dysrhythmia, hypotension, hypoxia, hemorrhage, renal insufficiency, or infection was evaluated in the study and control groups. Deaths within 3 and 30 days of the procedure and duration of survival after discharge from the hospital were recorded. Frequency of complications and 3- and 30-day mortality did not differ between the 2 groups. Duration of survival after discharge from the hospital in patients with HIV disease (7.4 +/- 9.7 months) was approximately 25 percent that in control patients (30.6 +/- 35.9 months) (p = 0.02). CONCLUSIONS: HIV disease does not increase the risk of postprocedural complications, including death, up to 30 days postprocedure. Thereafter, patients with HIV disease classified by the Walter Reed System as > or = 3B may survive for a shorter time than do equally ill patients who do not have HIV disease. Thus, needed surgical intervention should not be limited based on HIV status and concern for subsequent complications.

Adult↗
PubMed2002

[Study on the bacterial identification using 16S-23S rRNA gene spacer regions]

OBJECTIVE: To examine the use of PCR utilizing 16S-23S rRNA gene spacer regions in the identification of bacteria. METHODS Primers used in PCR were designed by using the target sequences from the genes encoding 16S-23S rRNA spacer regions. PCR was used for the detection of different standard and clinical bacterial strains. RESULTS Characteristic DNA maps were present after using the PCR to identify 27 standard strains from 27 species. The maps could be directly used for classification of the tested bacterial strains or further differentiated by RFLP. The sensitivity of the PCR may be as high as 2.5 CFU/ml. No non-specific amplification products were observed when using DNA from human PBMC funguses or viruses as templates. Thirty-two strains of bacteria isolated from clinical strains showed DNA maps similar to the DNA maps amplified from standard strains. CONCLUSION The PCR detection of bacteria using 16S-23S rRNA gene spacer regions is sensitive, rapid, specific and accurate for identification of bacteria and provides a new rapid method for determining the clinical diagnosis and the etiology of sepsis.

Journal Article↗
PubMed2000

Primary hepatocellular carcinoma in Australia, 1978-1997: increasing incidence and mortality.

OBJECTIVES: To describe trends in primary hepatocellular carcinoma (HCC) incidence and mortality in Australia between 1978 and 1997, and to delineate the effects of hepatitis B virus (HBV) and hepatitis C virus (HCV) infection by examining cases of HCC in Australian-born and overseas-born people separately. DESIGN AND SETTING: Retrospective analysis of national incidence and mortality data in which the underlying cause was coded as HCC (International classification of diseases, ninth revision [ICD-9] code 155.0). MAIN OUTCOME MEASURES: Changes in age-standardised HCC incidence rates in men and women between 1983 and 1996; age-standardised HCC death rates in Australian-born and overseas-born men and women between 1978 and 1997. RESULTS: Age-standardised incidence rates increased in men and women (from 2.06 and 0.57 per 100,000 respectively in 1983-1985 to 3.97 and 0.99 respectively in 1995-1996). Age-standardised death rates increased in Australian-born and overseas-born men and overseas-born women (from 1.43, 2.35 and 0.62 respectively per 100,000 in 1978-1982 to 2.50, 4.41 and 1.36 respectively in 1993-1997). However, death rates in Australian-born women did not increase (0.58 per 100,000 in 1978-1982 and 0.63 in 1993-1997). CONCLUSIONS: HCC incidence and death rates in Australia have increased over the past two decades, except in Australian-born women. A likely explanation for at least a portion of this increase is increased prevalences of HBV and HCV infection in Australia.

Age Factors↗
PubMed1982

Enumeration of antigenic sites of influenza virus hemagglutinin.

The antigenic sites on the hemagglutinin of X-31 (H3) influenza virus have been defined by using a competitive radioimmunoassay with a panel of monoclonal antibodies which includes those known to select variants with substitutions of particular amino acids. The capacity of each monoclonal antibody to block the binding of other radioiodinated monoclones to purified hemagglutinin permitted classification of the panel into four separate groups, each of which defined a particular antigenic site on the hemagglutinin molecule. Three of these are located on the polypeptide backbone and correspond to the "hinge," the "loop," and the "tip/interface" of the X-ray crystallographic model of Wiley et al. (Nature [London] 289:373-378, 1981). Nonreciprocal blocking of certain anti-interface antibodies by anti-loop antibody suggests that much of the exposed surface of the head of the hemagglutinin molecule extending from the loop to the interface may be a continuum of epitopes. A fourth antigenic site is carbohydrate in nature, presumably situated on the antigenic oligosaccharide side chains. These four domains are in addition to two antigenic sites defined by monoclonal antibodies that inhibit neither hemagglutination nor infectivity (Breschkin et al., Virology 113:130-140, 1981;' Yewdell et al., Nature [London] 279:246-248, 1979).

Antibodies, Monoclonal↗
PubMed1982

Molecular biology of rotaviruses. III. Isolation and characterization of temperature-sensitive mutants of bovine rotavirus.

Twenty-six temperature-sensitive (ts) mutants of United Kingdom tissue culture-adapted bovine rotavirus were isolated and characterized. Fourteen of these mutants were determined to be ts both by efficiency of plating and by virus yield at the nonpermissive temperature of 39.5 degrees C as compared with that at the permissive temperature of 32 degrees C. The remaining mutants were only ts by the criterion of efficiency of plating. High-frequency recombination (gene reassortment) was observed when some pairs of mutants were crossed, and this allowed the classification of the mutants into five separate recombination groups. Groups III and V have prototype ts mutants (ts34 and ts115, respectively) that do not synthesize RNA or polypeptides at 39.5 degrees C. The other groups, I, II, and IV, have prototype mutants (ts17, ts7, and ts6, respectively) that synthesize both RNA and polypeptides at 39.5 degrees C, although ts17 does so only at a reduced level.

Cytopathogenic Effect, Viral↗
PubMed1983

[Study of virus-associated lymphomas in primates using a model of malignant lymphoma of the baboon].

An outbreak of malignant lymphoma was registered in a population of hamadryas baboons. Animals inoculated with blood from patients with various forms of leukemia were planted into the stock 10 years ago. 218 out of 3219 animals have already died from lymphoma. The morphological pattern of horizontally-spreading lymphoma was similar to basic cell patterns of Hodgkin's and non-Hodgkin lymphoma in man. As far as the immunologic classification of tumor lymphoid cells is concerned, baboon lymphomas were of B-cell, T-cell and neither T- nor B-cell types. Xenotropic and ecotropic endogenous oncoviruses and lymphotropic herpesvirus of the baboon were isolated from cell cultures of healthy and sick animals. The said herpesvirus was closely related to a human one, both belonging to a family of primate lymphotropic herpesviruses. Plasma residue of the sick animals contained C-type oncovirus which immunologically differed from that of baboon endogenous oncovirus. Blood serum of nearly all sick baboons and those in the stock at high risk for lymphoma contained antibodies which entered into immunofluorescence reaction with antigens of HTLV virus-producing cells. Similar antibodies at a low titer concentration were identified only in individual lymphoma-free baboons in control. The relationship between HTLV virus and C-type oncovirus as well as their relevance to human hemoblastosis are being under study.

Animals↗
PubMed1981

Classification of avian paramyxoviruses by immunodiffusion on the basis of antigenic specificity of their M protein antigens.

Seventeen avian paramyxoviruses consisting of ten reference strains and seven recent isolates were classified by immunodiffusion into six species on the basis of the antigenic specificity of their M protein (MP) antigens. The species were represented by the following viruses. (1) Newcastle disease virus, (2) Chicken/California/Yucaipa/56, (3) Turkey/Wisconsin/68, (4) Duck/Mississippi/75, (5) Pigeon/Otaru/76 and (6) Budgerigar/Kunitachi/1/74. The differences in the HN antigens between viruses which were classified into the same species on the basis of the antigenic specificity of their MP antigens, may provide a basis for classifying them into types.

Antigens, Viral↗
PubMed1984

Classification of herpesvirus saimiri into three groups based on extreme variation in a DNA region required for oncogenicity.

The leftmost 7 kilobase pairs of unique sequence L-DNA of herpesvirus saimiri was found to be highly variable among different strains as determined by restriction endonuclease analysis and blot hybridization. This region in one group of viruses (group A) showed only very weak hybridization with the DNA of two other groups. Similarly, a fragment of group B hybridized to DNA of its own group much more strongly than to group A. No homology was detected within a 1.2-kilobase-pair region between strain 11 (group A virus) and strain SMHI (group B) even under reduced stringency, and the adjacent 5.5-kilobase-pair segment of the region showed only a very weak intergroup hybridization. DNA of a third group of viruses (non-A, non-B) did not hybridize significantly with cloned fragments representing the leftmost 7-kilobase-pair region of either group A or group B. Since sequences in the highly variable region are required for the oncogenicity of the virus, these results raise interesting questions regarding the origin and function of this region of the genome.

Animals↗